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Diffstat (limited to 'sci-biology/ncbi-tools/ncbi-tools-2.2.26-r3.ebuild')
| -rw-r--r-- | sci-biology/ncbi-tools/ncbi-tools-2.2.26-r3.ebuild | 169 |
1 files changed, 169 insertions, 0 deletions
diff --git a/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r3.ebuild b/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r3.ebuild new file mode 100644 index 000000000000..cec2f688b661 --- /dev/null +++ b/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r3.ebuild @@ -0,0 +1,169 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit epatch flag-o-matic prefix toolchain-funcs + +DESCRIPTION="Development toolkit and applications for computational biology, including BLAST" +HOMEPAGE="https://www.ncbi.nlm.nih.gov/" +SRC_URI="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/${PV}/ncbi.tar.gz -> ${P}.tar.gz" + +SLOT="0" +LICENSE="public-domain" +KEYWORDS="~alpha amd64 ppc64 x86 ~amd64-linux ~x86-linux ~ppc-macos" +IUSE="doc static-libs X" + +RDEPEND=" + app-shells/tcsh + dev-lang/perl + media-libs/libpng:0= + virtual/glu + virtual/opengl + X? ( + media-libs/fontconfig + x11-libs/motif:0= + x11-libs/libICE + x11-libs/libX11 + x11-libs/libXft + x11-libs/libXmu + x11-libs/libXt + )" +DEPEND=" + ${RDEPEND} + virtual/pkgconfig +" + +S="${WORKDIR}/ncbi" + +EXTRA_VIB="asn2all asn2asn" + +pkg_setup() { + echo + ewarn 'Please note that the NCBI toolkit (and especially the X' + ewarn 'applications) are known to have compilation and run-time' + ewarn 'problems when compiled with agressive compilation flags. The' + ewarn '"-O3" flag is filtered by the ebuild on the x86 architecture if' + ewarn 'X support is enabled.' + echo +} + +src_prepare() { + epatch \ + "${FILESDIR}"/${PN}-extra_vib.patch \ + "${FILESDIR}"/${P}-bfr-overflow.patch \ + "${FILESDIR}"/${P}-format-security.patch \ + "${FILESDIR}"/${P}-_DEFAULT_SOURCE.patch + + if use ppc || use ppc64; then + epatch "${FILESDIR}"/${PN}-lop.patch + fi + + if ! use X; then + sed \ + -e "s:\#set HAVE_OGL=0:set HAVE_OGL=0:" \ + -e "s:\#set HAVE_MOTIF=0:set HAVE_MOTIF=0:" \ + -i "${S}"/make/makedis.csh || die + else + # X applications segfault on startup on x86 with -O3. + use x86 || replace-flags '-O3' '-O2' + fi + + # Apply user C flags... + cd "${S}"/platform + sed \ + -e "s:-O[s0-9]\?::g" \ + -e 's:-m\(cpu\|arch\)=[a-zA-Z0-9]*::g' \ + -e 's:-x[A-Z]*::g' \ + -e 's:-pipe::g' \ + -e "/NCBI_MAKE_SHELL *=/s:=.*:= \"${EPREFIX}/bin/sh\":g" \ + -e "/NCBI_AR *=/s:ar:$(tc-getAR):g" \ + -e "/NCBI_RANLIB *=/s:ranlib:$(tc-getRANLIB):g" \ + -e "/NCBI_CC *=/s:= [a-zA-Z0-9]* := $(tc-getCC) :g" \ + -e "/NCBI_OPTFLAG *=/s:$: ${CFLAGS}:g" \ + -e "/NCBI_LDFLAGS1 *=/s:$: ${CFLAGS} ${LDFLAGS}:g" \ + -e "/NCBI_OGLLIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --cflags gl glu 2>/dev/null):g" \ + -e "/OPENGL_LIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --libs gl glu 2>/dev/null):g" \ + -e "/NCBI_OGLLIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --libs gl glu 2>/dev/null):g" \ + -i * || die + + # We use dynamic libraries + sed -i -e "s/-Wl,-Bstatic//" *linux*.ncbi.mk || die + + sed \ + -re "s:/usr(/bin/.*sh):\1:g" \ + -e "s:(/bin/.*sh):${EPREFIX}\1:g" \ + -i $(find "${S}" -type f) || die +} + +src_compile() { + export EXTRA_VIB + cd "${WORKDIR}" + csh ncbi/make/makedis.csh || die + mkdir "${S}"/cgi "${S}"/real || die + mv "${S}"/bin/*.cgi "${S}"/cgi || die + mv "${S}"/bin/*.REAL "${S}"/real || die + cd "${S}"/demo + emake \ + -f ../make/makenet.unx \ + CC="$(tc-getCC) ${CFLAGS} -I../include -L../lib" \ + LDFLAGS="${LDFLAGS}" \ + spidey + cp spidey ../bin/ || die +} + +src_install() { + #sci-geosciences/cdat-lite + mv "${S}"/bin/cdscan "${S}"/bin/cdscan-ncbi || die + + dobin "${S}"/bin/* + + for i in ${EXTRA_VIB}; do + dobin "${S}"/build/${i} + done + use static-libs && dolib.a "${S}"/lib/*.a + mkdir -p "${ED}"/usr/include/ncbi + cp -RL "${S}"/include/* "${ED}"/usr/include/ncbi || \ + die "Failed to install headers." + + # TODO: wwwblast with webapps + #insinto /usr/share/ncbi/lib/cgi + #doins ${S}/cgi/* + #insinto /usr/share/ncbi/lib/real + #doins ${S}/real/* + + # Basic documentation + dodoc "${S}"/{README,VERSION,doc/{*.txt,README.*}} + newdoc "${S}"/doc/fa2htgs/README README.fa2htgs + newdoc "${S}"/config/README README.config + newdoc "${S}"/network/encrypt/README README.encrypt + newdoc "${S}"/network/nsclilib/readme README.nsclilib + newdoc "${S}"/sequin/README README.sequin + mv "${S}"/doc/man/fmerge{,-ncbi}.1 || die + doman "${S}"/doc/man/* + + # Hypertext user documentation + dohtml "${S}"/{README.htm,doc/{*.html,*.htm,*.gif}} + insinto /usr/share/doc/${PF}/html + doins -r "${S}"/doc/blast "${S}"/doc/images "${S}"/doc/seq_install + + # Developer documentation + if use doc; then + # Demo programs + mkdir "${ED}"/usr/share/ncbi + mv "${S}"/demo "${ED}"/usr/share/ncbi/demo || die + fi + + # Shared data (similarity matrices and such) and database directory. + insinto /usr/share/ncbi + doins -r "${S}"/data + dodir /usr/share/ncbi/formatdb + + # Default config file to set the path for shared data. + insinto /etc/ncbi + newins "${FILESDIR}"/ncbirc .ncbirc + eprefixify "${ED}"/etc/ncbi/.ncbirc + + # Env file to set the location of the config file and BLAST databases. + newenvd "${FILESDIR}"/21ncbi-r1 21ncbi +} |